Welcome to the HIV forum. These comments repond both to your question above and the follow-up ones below.
With the standard HIV tests in common use in the US and other industrialized countries, around 90% of newly infected people have positive tests by that time. Although there is a slight chance that a later test would be positive, it is very unlikely. In addition, all your exposures have been enther completely protected or oral, which is zero risk or close to it. The combination of low risk exposures plus the negative blood test is nearly 100% proof you aren't infected, regardless of your flu-like symptoms. However, to be completely certain, you should ask your health care provider about having a follow-up HIV test around 6-8 weeks after the exposure.
Of course it is possible to catch genital herpes from oral sex. Half of all new cases of genital herpes in recent years have been due to HSV-1, the virus that is responsible for oral herpes -- which is carried by half of all adults. However, I agree with your urologist, the your penile pimple most likely wasn't herpes, which doesn't usally cause the deeper sort of pus-filled, pimple-like lesion you describe. In any case, oral shedding of HSV-1 is quite uncommon in the absence of overt oral herpes outbreaks, so the transmission risk for any single exposure is low if the oral partner doesn't have a cold sore. For a more detailed discussion, go to the STD forum and use the search function to look for "herpes symptoms". HPV is rarely if ever transmitted by oral sex.
Here is an older thread with more discussion of STD and HIV risks from oral sex:
http://www.medhelp.org/posts/STDs/STD-risk-from-receiving-oral-sex/show/669224
You also can enter such terms as "oral sex and STDs" or "HIV and oral sex" in the search windows of this forum or the STD forum. You will find hundreds of discussions, maybe a couple thousand.
My final suggestion concerns sexual safety in general. It sounds like you're going about it pretty well. However, you don't mention one of the most important aspects of safe sex for men having sex with men: always ask about and share your own HIV status, before having sex, and avoid sex (and certainly avoid unprotected anal sex) with partners who are positive, don't know, or seem evasive in their answers. Even when safe sex is planned, remember that condoms break or can be forgotten in the heat of the moment. In the long run, "do ask, do tell" is just as important in preventing as consistent condom use for anal sex. (Maybe you do this now -- in which case, congratulations. But I repeat this message whenever I get the chance, for all forum users to see.)
Good luck. Stay safe-- HHH, MD